University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 2005 Coral Reef Assessment: An Index Utilizing Sediment Constituents Camille A. Daniels University of South Florida Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the American Studies Commons Scholar Commons Citation Daniels, Camille A., "Coral Reef Assessment: An Index Utilizing Sediment Constituents" (2005). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/2847 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Coral Reef Assessment: An Index Utilizing Sediment Constituents by Camille A. Daniels A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science University of South Florida Major Professor: Pamela Hallock-Muller, Ph.D David Mann, Ph.D Carl Beaver, Ph.D Maya Trotz, Ph.D Date of Approval: July 25, 2005 Keywords: SEDCON, community structure, bioerosion, water quality, bioindicator © Copyright 2005, Camille Daniels ACKNOWLEDGEMENTS I am grateful for the diligent efforts and support of my major professor, Dr. Pamela Hallock Muller. She sets the precedent for being an excellent advisor and mentor, and I am honored to work with her. I also thank my committee, Carl Beaver, David Mann, and Maya Trotz for their time and critical perspective during the review of my thesis. The Florida Fish and Wildlife Research Institute Coral Reef Team (FWRI-CRT) collected sediment samples at the Coral Reef Evaluation and Monitoring Program (CREMP) sites in the Florida Keys National Marine Sanctuary. Special thanks go to Walter Jaap, longtime member of the FWRI-CRT for initiating the sediment sampling at CREMP sites in 2001, for his expertise and advice, for providing data access, and also for collecting the samples from the Florida Middle Grounds. Michael Callahan (FWRI-CRT) contributed information and assistance throughout this project, including sample collection at CREMP sites and the Florida Middle Grounds. Dr. Dana E. Williams of NOAA, Miami, FL provided sediment samples and associated data from Navassa. I greatly appreciate my colleagues in the Reef Indicators Lab for their endless support and generosity, especially Libby Carnahan and Beth Fisher, who collected the samples from Key Largo (FKNMS permit number 2003-002). Many thanks to Barbara Lidz and Nicole Caesar at the U.S.Geological Survey, and to Heidi Souder at the Center for Ocean Technology, all in St. Petersburg. The SEDCON Index was proposed during bioindicator research funded by the U.S. Environmental Protection Agency – ORD-NCER "Science to Achieve Results Program” (STAR-GAD-R825869), P. Hallock Muller, Principal Investigator. Development of the SEDCON Index was supported by the National Oceanic and Atmospheric Administration/National Undersea Research Center UNCW Subcontract 2003-24A. Water quality data were provided by the SERC/FIU Water Quality Monitoring Network, which is supported by SFWMD/SERC Cooperative Agreements #C-10244 and #C-13178, as well as EPA Agreement #X994621-94-0. Thanks to Dr. Ashanti Pyrtle for her guidance and funding through the NSF-FGLSAMP Bridge to the Doctorate Program, and the Von Rosenstiels for their financial support of students at the College of Marine Science. My graduate career would not have been possible without the help and encouragement of Dr. Paul LaRock at Louisiana State University. This manuscript is dedicated to my parents and sisters, whose love, support, and inspiration, motivate me to achieve. TABLE OF CONTENTS LIST OF TABLES....................................................................................................... iii LIST OF FIGURES ..................................................................................................... vi ABSTRACT............................................................................................................... viii INTRODUCTION .........................................................................................................1 The SEDCON Index ..........................................................................................5 Assessment Relevance.......................................................................................7 Ecological Relevance.........................................................................................9 Whole Grain or Thin Section Analysis? ..........................................................10 PROJECT OBJECTIVES ............................................................................................11 METHODS ..................................................................................................................12 Study Sites .......................................................................................................12 Water Quality Data ..........................................................................................18 Sediment Analyses...........................................................................................19 Statistical Analyses ..........................................................................................23 RESULTS ....................................................................................................................25 Grain Size Analysis..........................................................................................25 Constituent Analysis ........................................................................................31 SIMPER Analyses ...........................................................................................40 SEDCON INDEX CALCULATION...........................................................................50 RESULTS OF INDEX CALCULATIONS.................................................................53 Inter-region evaluation for CREMP sites ........................................................64 Comparison of SI with benthic cover data.......................................................67 Water quality comparisons ..............................................................................71 DISCUSSION..............................................................................................................74 Bias and grain size ...........................................................................................74 Sediment composition......................................................................................75 SEDCON Index equation.................................................................................76 Synthesis of constituent data and index values................................................77 Temporal trends ...............................................................................................78 Coral Cover......................................................................................................79 Influence of Abiotic Parameters ......................................................................81 Strengths and Restrictions................................................................................82 i Future investigation and Recommendations....................................................83 CONCLUSIONS..........................................................................................................84 REFERENCES ............................................................................................................85 APPENDICES .............................................................................................................92 Appendix I PCA eigenvectors and values for 2001 CREMP sites ..........93 Appendix II Materials and Methods for SEDCON Index sample Processing .............................................................................95 Appendix III SEDCON Index procedure ...................................................96 ii LIST OF TABLES Table 1 Categories of sediment constituents used for the SEDCON Index........5 Table 2 Description of Key Largo area site samples; abbreviations are used in text and subsequent figures and tables.............................................17 Table 3 Depths for Florida Middle Grounds and Navassa sites .......................17 Table 4 SERC Water Quality Monitoring Network sampling list (Boyer and Jones, 2002; Callahan, 2005) ........................................................18 Table 5 CREMP sites with associated water quality stations (adapted from Callahan, 2005)....................................................................................19 Table 6 Roles of carbonate producers in reef community structure and the SEDCON Index..............................................................................22 Table 7 Scale for particle size fractionation for sediment samples (Wentworth, 1922)...............................................................................25 Table 8 Grain size data for Key Largo samples for intrasite comparison ( bold indicates median grain size; KL- represents Key Largo)...........26 Table 9 Grain size data for all CREMP sites ( bold indicates median grain size).....................................................................................................27 Table 10 Grain size data for Florida Middle Grounds samples ( bold indicates median grain size)................................................................................30